ClinVar Miner

Submissions for variant NM_003742.4(ABCB11):c.390-1G>T

dbSNP: rs1558917090
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000729596 SCV000857270 pathogenic not provided 2017-10-05 criteria provided, single submitter clinical testing
Baylor Genetics RCV003461004 SCV004216318 likely pathogenic Benign recurrent intrahepatic cholestasis type 2 2023-09-13 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000729596 SCV004637223 likely pathogenic not provided 2022-12-31 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 5 of the ABCB11 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ABCB11 are known to be pathogenic (PMID: 18395098, 20232290). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with cholestasis (PMID: 18395098). ClinVar contains an entry for this variant (Variation ID: 594334). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
PreventionGenetics, part of Exact Sciences RCV003965512 SCV004781664 likely pathogenic ABCB11-related disorder 2024-01-03 no assertion criteria provided clinical testing The ABCB11 c.390-1G>T variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. A different nucleotide substitution at this position (c.390-1G>A) was previously reported in the homozygous state in one individual with intrahepatic cholestasis (Strautnieks et al. 2008. PubMed ID: 18395098). Variants that disrupt the consensus splice acceptor site in ABCB11 are expected to be pathogenic. The c.390-1G>T variant is interpreted as likely pathogenic.

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